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annotate qualitymetrics_config.xml @ 1:6d3b7b6573d8 draft

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planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 60328240b89497f9dc7633b10b2a550b10da00c7
author ethevenot
date Fri, 21 Oct 2016 12:56:22 -0400
parents b4f5b5bc01dd
children 596320b84315
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6d3b7b6573d8 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 60328240b89497f9dc7633b10b2a550b10da00c7
ethevenot
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1 <tool id="quality_metrics" name="Quality Metrics" version="2.2.6">
0
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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2 <description>Metrics and graphics to check the quality of the data</description>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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4 <requirements>
1
6d3b7b6573d8 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 60328240b89497f9dc7633b10b2a550b10da00c7
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5 <requirement type="package" version="3.3.1">R</requirement>
0
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6 <requirement type="package">r-batch</requirement>
1
6d3b7b6573d8 planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 60328240b89497f9dc7633b10b2a550b10da00c7
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7 <requirement type="package">bioconductor-ropls</requirement>
0
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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8 </requirements>
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b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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10 <stdio>
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11 <exit_code range="1:" level="fatal" />
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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12 </stdio>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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13
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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14 <command><![CDATA[
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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15 Rscript $__tool_directory__/qualitymetrics_wrapper.R
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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16 dataMatrix_in "$dataMatrix_in"
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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17 sampleMetadata_in "$sampleMetadata_in"
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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18 variableMetadata_in "$variableMetadata_in"
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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19
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20 CV "${CV_condition.CV}"
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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21 #if str($CV_condition.CV ) == 'TRUE':
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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22 Compa "${CV_condition.Compa}"
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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23 seuil "${CV_condition.seuil}"
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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24 #else:
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25 Compa "TRUE"
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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26 seuil "1"
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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27 #end if
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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28
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29 #if $advPar.optC == "full"
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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30 poolAsPool1L "$advPar.poolAsPool1L"
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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31 #else:
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32 poolAsPool1L "TRUE"
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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33 #end if
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34
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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35 sampleMetadata_out "$sampleMetadata_out"
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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36 variableMetadata_out "$variableMetadata_out"
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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37 figure "$figure"
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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38 information "$information"
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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39 ]]></command>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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40
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41 <inputs>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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42 <param name="dataMatrix_in" type="data" label="Data matrix file" help="" format="tabular" />
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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43 <param name="sampleMetadata_in" type="data" label="Sample metadata file" help="" format="tabular" />
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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44 <param name="variableMetadata_in" type="data" label="Variable metadata file" help="" format="tabular" />
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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45
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46 <conditional name="CV_condition">
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47 <param name="CV" type="select" label="Coefficient of Variation" help="">
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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48 <option value="FALSE">no</option>
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49 <option value="TRUE">yes</option>
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50 </param>
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51 <when value="TRUE">
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52 <param name="Compa" label="Which type of CV calculation should be done" type="select" display="radio" help="">
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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53 <option value="TRUE">ratio between pool and sample CVs</option>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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54 <option value="FALSE">only pool CV</option>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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55 </param>
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56 <param name="seuil" type="float" label="Threshold" value="1.25" min="0.0000000000000001" help="if comparing pool and sample CVs, corresponds to the max ratio tolerated (basically between 1.0 and 1.25) ; else corresponds to the max pool CV tolerated (basically 0.3)"/>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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57 </when>
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58 <when value="FALSE">
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59 <param name="Compa" type="hidden" value="TRUE"/>
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60 <param name="seuil" type="hidden" value="1"/>
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61 </when>
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62 </conditional>
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63
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64 <conditional name="advPar">
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65 <param name="optC" type="select" label="Advanced parameters" >
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66 <option value="default" selected="true">Use default</option>
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67 <option value="full">Full parameter list</option>
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68 </param>
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69 <when value="full">
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70 <param name="poolAsPool1L" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Use 'pool' samples as 'pool1' when computing the correlation with dilution?"/>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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71 </when>
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72 <when value="default">
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73 <param name="poolAsPool1L" type="hidden" value="TRUE"/>
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74 </when>
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75 </conditional>
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76
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77 </inputs>
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78
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79 <outputs>
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80 <data name="sampleMetadata_out" label="${tool.name}_${sampleMetadata_in.name}" format="tabular" ></data>
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81 <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data>
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82 <data name="figure" label="${tool.name}_figure.pdf" format="pdf"/>
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83 <data name="information" label="${tool.name}_information.txt" format="txt"/>
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84 </outputs>
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85
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86 <tests>
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87 <test>
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88 <param name="dataMatrix_in" value="input-dataMatrix.tsv"/>
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89 <param name="sampleMetadata_in" value="input-sampleMetadata.tsv"/>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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90 <param name="variableMetadata_in" value="input-variableMetadata.tsv"/>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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91 <param name="CV" value="FALSE"/>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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92 <param name="optC" value="default"/>
b4f5b5bc01dd planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 73366dd3473c509341ab9ba1df8ba748d08a50a1
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93 <output name="sampleMetadata_out" file="output-sampleMetadata.tsv"/>
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94 <output name="variableMetadata_out" file="output-variableMetadata.tsv"/>
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95 </test>
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96 </tests>
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97
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98 <help>
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99
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100 .. class:: infomark
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101
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102 **Authors** Marion Landi, Melanie Petera and Etienne Thevenot (W4M Core Development Team)
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103
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104 ---------------------------------------------------
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105
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106 .. class:: infomark
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107
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108 **Tool updates**
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109
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110 See the **NEWS** section at the bottom of this page
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111
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112 ---------------------------------------------------
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113
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114 .. class:: infomark
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115
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116 **References**
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117
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118 | Thevenot EA., Roux A., Xu Y., Ezan E., and Junot C. (2015). Analysis of the human adult urinary metabolome variations with age, body mass index and gender by implementing a comprehensive workflow for univariate and OPLS statistical analyses. *Journal of Proteome Research*, **14**:3322-3335 (http://dx.doi.org/10.1021/acs.jproteome.5b00354)
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119 | Mason R., Tracy N. and Young J. (1997). A practical approach for interpreting multivariate T2 control chart signals. *Journal of Quality Technology*, **29**:396-406.
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120 | Alonso A., Julia A., Beltran A., Vinaixa M., Diaz M., Ibanez L., Correig X. and Marsal S. (2011). AStream: an R package for annotating LC/MS metabolomic data. *Bioinformatics*, **27**:1339-1340. (http://dx.doi.org/10.1093/bioinformatics/btr138)
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121
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122 ---------------------------------------------------
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123
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124 ========================
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125 Quality Metrics
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126 ========================
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127
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128 -----------
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129 Description
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130 -----------
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131
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132 | The **Quality Metrics** tool provides quality metrics of the samples and variables, and visualization of the data matrix
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133 | The optional *Coefficient of Variation* arguments allows to flag the variables with a pool CV (or a pool CV over sample CV ratio) above a specific threshold
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134 | The advanced *PoolAsPool1* argument is used when correlations with pool dilutions are computed: When set to TRUE [default], samples indicated as "pool" will be considered as "pool1" for the correlation together with the other pool dilutions (e.g. "pool2", "pool4", etc.); otherwise, "pool" samples will not be considered to compute the correlation (this enables the experimenter to have distinct "pool" samples for the computation of CV and "pool1" samples for the computation of dilution)
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135 | The **sampleMetadata** is returned as output with 3 additional columns containing the p-values for the Hotellings'T2 and Z-scores of intensity deciles and proportion of missing values
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136 | The **variableMetadata** is returned as output; in case a **sampleType** column is included in the input sampleMetadata file, additional columns will be added to indicate the variable quality metrics (eg mean, sd, CV on 'pool', 'sample' or 'blank', or correlation with pool dilutions, depending on the known type present in the 'sampleType' column)
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137 | A **figure** is generated (pdf file) which illustrates the main computed sample and variable metric values
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138
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139
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140
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141 -----------------
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142 Workflow position
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143 -----------------
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144
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145 .. image:: QualityControl.png
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146 :width: 800
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147
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148
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149
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150 -----------
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151 Input files
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152 -----------
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153
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154 +----------------------------+---------+
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155 | Parameter : num + label | Format |
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156 +============================+=========+
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157 | 1 : Data matrix file | tabular |
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158 +----------------------------+---------+
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159 | 2 : Sample metadata file | tabular |
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160 +----------------------------+---------+
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161 | 3 : Variable metadata file | tabular |
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162 +----------------------------+---------+
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163
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164 ----------
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165 Parameters
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166 ----------
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167
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168 Data matrix
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169 | contains the intensity values of the variables.
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170 |
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171
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172 Sample metadata file
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173 | contains the metadata of the samples; in particular
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174 | when the 'sampleType' column is available, with known types such as 'blank', 'sample', 'pool', 'poolN' (where N is a dilution factor of the pool), metrics will be computed (eg mean, sd, CV, correlation with the dilution factor, etc) for each variable (see the 'PoolAsPool1' argument below)
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175 | 'pool' (and 'sample') should be present in the 'sampleType' column when setting the 'coefficient of variation' to TRUE
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176 |
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177
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178 Variable metadata file
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179 | contains variable information.
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180 |
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181
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182 Note:
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183 | Required formats for the dataMatrix, sampleMetadata, and variableMetadata files are described in the **HowTo** entitled 'Format Data For Postprocessing' available on the main page of Workflow4Metabolomics.org; the formats of the 3 tables can be further checked with the **Check Format** module
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184 |
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185
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186 Coefficient of Variation
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187 | If 'yes' (not default): variables are classed according to the Coefficient of Variation (CV)
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188 | i.e.: CV of pools (and CV of samples if needed) are calculated and compared to a defined threshold;
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189 | then variables are classed with a 0/1 coding.
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190 |
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191
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192 Which type of CV calculation should be done (only if CV=yes)
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193 | Type of CV comparison that will be used.
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194 | 'ratio between pool and sample CVs' **OR** 'only pool CV'
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195 |
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196
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197 Threshold (only if CV=yes)
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198 | If comparing pool and sample CVs, corresponds to the max ratio tolerated (basically between 1.0 and 1.25).
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199 | Else corresponds to the max pool CV tolerated (basically 0.3).
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200 |
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201
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202 PoolAsPool1 (Advanced parameter)
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203 | If 'poolN' (where N is a dilution factor) sample types are present in the 'sampleType' column of the sample metadata file, the Pearson correlation of the intensity with the dilution factor is computed for each variable; the 'PoolAsPool1' parameter indicates whether samples of 'pool' types should be considered as 'pool1' (and hence included in the computation of dilution correlations); default is TRUE
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204
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205
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206 ------------
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207 Output files
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208 ------------
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209
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210
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211 sampleMetadata.tabular
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212 | tsv output
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213 | 3 additional columns have been added to the input sampleMetadata file and contain the **p-values** of
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214 | 1) the **Hotelling's T2** test in the first plane of PC components (Mason et al, 1997)
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215 | 2) the **Z-score** of **intensity deciles** (Alonso et al, 2011)
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216 | 3) the **Z-score** of the proportion of **missing values** (Alonso et al, 2011)
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217 | for each test, low p-values indicate samples with extreme behaviour
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218 |
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219
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220 variableMetadata.tabular
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221 | tsv output
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222 | When the type of samples is available (ie the **sampleType** column is included in the input sampleMetadata file), variable metrics are computed: **sample**, **pool**, and **blank** **mean**, **sd** and **CV** (if the corresponding types are present in the 'sampleType' column), as well as **'blank' mean / 'sample' mean**, and **'pool' CV / 'sample' CV ratio**
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223 | If pool dilutions have been used and are indicated in the 'sampleType' column as **poolN** where N is an integer indicating the dilution factor (eg **pool2** for a two-fold dilution of the pool; note that the non-diluted pool remains indicated as 'pool') the Pearson **correlation** (and corresponding p-value) between the intensity and the dilution factor is computed for each variable.
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224 | When the **Coefficient of variation** argument is set to 'TRUE', the variableMetadata begins with 2 (or 3) columns indicating the pool CV (and the sample CV) and if the pool CV (or the ratio between pool CV and sample CV) is above the selected threshold
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225 |
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226
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227 figure.pdf
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228 | Figure summarizing the various values of the computed metrics and tests; includes several visualizations of the samples (eg, PCA scores) and intensities (eg, image of the data matrix)
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229 |
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230
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231 information.txt
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232 | Text file with informations regarding the metrics computed, eg those depending on the availability of the 'sampleMetadata' column, and specific types such as 'sample', 'pool', pool dilutions ('poolN'), or 'blank'
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233 |
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234
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235
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236 ---------------------------------------------------
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237
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238 ---------------
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239 Working example
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240 ---------------
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241
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242 |
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243
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244 .. class:: infomark
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245
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246 See the **W4M00001b_sacurine-complete** shared history in the **Shared Data/Published Histories** menu (https://galaxy.workflow4metabolomics.org/history/list_published)
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247
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248 ---------------------------------------------------
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249
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250 ----
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251 NEWS
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252 ----
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253
1
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254 CHANGES IN VERSION 2.2.6
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255 ========================
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256 MINOR MODIFICATION
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257
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258 Graphic: pool_CV inferior to 30%: pools with a NaN value are now counted as having a superior to 30% value (to avoid generating an NA metric value)
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259
0
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260 CHANGES IN VERSION 2.2.4
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261 ========================
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262
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263 Additional running and installation tests added with planemo, conda, and travis
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264
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265 CHANGES IN VERSION 2.2.3
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266 ========================
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267
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268 INTERNAL MODIFICATIONS
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269
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270 Modifications of the **qualitymetrics_script.R** file to handle the recent **ropls** package versions (i.e. 1.3.15 and above) which use S4 classes
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271
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272 Creating tests for the R code
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273
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274 CHANGES IN VERSION 2.2.2
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275 ========================
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276
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277 Minor internal changes
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278
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279
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280 </help>
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281
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282 <citations>
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283 <citation type="doi">10.1021/acs.jproteome.5b00354</citation>
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284 <citation type="doi">10.1093/bioinformatics/btr138</citation>
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285 <citation type="bibtex">@Article{Mason1997,
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286 Title = {A practical approach for interpreting multivariate T2 control chart signals},
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287 Author = {Mason, RL. and Tracy, ND. and Young, JC.},
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288 Journal = {Journal of Quality Technology},
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289 Year = {1997},
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290 Number = {4},
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291 Pages = {396-406},
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292 Volume = {29},
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293 }</citation>
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294 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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295 </citations>
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296
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297 <!--
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298
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299 Input files
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300 ===========
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301
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302 | **To generate the "dataMatrix", "sampleMetadata" and "variableMetadata" files:**
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303 | **1) copy/paste the values below in three distinct .txt files**
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304 | **2) use the "Get Data" / "Upload File" in the "Tools" (left) panel from the Galaxy page by choosing:**
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305 | **Convert spaces to tabs: 'Yes'**
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306 |
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307
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308 **dataMatrix file**::
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309
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310 dataMatrix QC_4 sam_44 sam_18 sam_23 blk_3 sam_9 sam_22 QC_6 blk_4
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311 met_031 5601185.9 4446133.4 4144765.4 3085899.9 NA 6748534.9 5819543.8 3256720.3 NA
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312 met_032 4.07 4.08 4.11 4.1 NA 4.04 4.13 4.11 NA
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313 met_033 1448205184 1456986135 993364802.3 1162711600 5569143.2 1043559922 1465003454 1052094028 5247494.3
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314 met_034 4.11 4.21 4.18 4.1 4.09 4.1 4.14 4.11 4.08
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315 met_035 3777580.7 2296751 1890711.7 1767424.6 6567.5 1906253.5 3043253.9 2856958.5 7940.8
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316 met_036 4.12 4.21 4.26 4.1 4.11 4.22 4.27 4.12 4.2
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317 met_037 4982658.7 3751181.8 4219033.2 2425759.9 NA 11978184.4 4306459.5 3352187 NA
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318 met_038 4.45 4.38 4.4 4.4 NA 4.44 4.46 4.32 NA
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319 met_039 6658087.7 3231434.7 2932986.5 4098788.3 NA 3691132.6 6108614.4 4541941.9 NA
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320 met_040 4.49 4.56 4.48 4.5 NA 4.45 4.54 4.46 NA
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321
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322 **sampleMetadata file**::
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323
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324 sampleMetadata injectionOrder batch sampleType
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325 QC_4 19 batch1 pool
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326 sam_44 20 batch1 sample
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327 sam_18 23 batch1 sample
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328 sam_23 27 batch1 sample
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329 blk_3 31 batch1 blank
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330 sam_9 34 batch1 sample
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331 sam_22 38 batch1 sample
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332 QC_6 42 batch1 pool
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333 blk_4 43 batch1 blank
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334
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335 **variableMetadata file**::
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336
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337 variableMetadata number
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338 met_031 31
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339 met_032 32
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340 met_033 33
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341 met_034 34
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342 met_035 35
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343 met_036 36
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344 met_037 37
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345 met_038 38
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346 met_039 39
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347 met_040 40
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348
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349 Figure output
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350 =============
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351
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352 | You should obtain with this very simplified dataset the following figure:
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353 |
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354
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355 .. image:: qualitymetrics_workingExampleImage.png
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356 :width: 600
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357
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358 -->
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359
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360 </tool>